VMD-L Mailing List

From: Sabuj Pattanayek (sabuj.pattanayek_at_Vanderbilt.Edu)
Date: Thu May 12 2005 - 18:08:43 CDT

Hi,

Yes, I get the same licorice crash when running vmd 1.8.3 with "setenv
VMDSIMPLEGRAPHICS 1". I sent a the error report to linux-bugs_at_nvidia.com
some time ago, but without the generated system information from
nvidia-bug-report.sh. I never received a reply. I'll resend this time
with the system information.

I also tried getting a backtrace from vmd when it crashes but I could
not. It may have something to do with the fact that vmd uses SIGABRT
instead of SIGSEGV or maybe it's compiled with too many optimizations
and no -g flag?

I was able to get a backtrace from pymol however and I'm sure the
problem is very similar to vmd's. It looks like the function
glXChannelRectSyncSGIX () from /usr/lib/opengl/nvidia/lib/libGL.so.1 is
trying to allocate some bogus memory addresses/pointers which is causing
the program to crash in mallopt () from /lib/libc.so.6 . Here's the
backtrace, sorry if its really long:

 OpenGL-based graphics engine:
  GL_VENDOR: NVIDIA Corporation
  GL_RENDERER: Quadro4 750 XGL/AGP/SSE/3DNOW!
  GL_VERSION: 1.5.3 NVIDIA 71.74
 Hardware stereo capability detected.
[New Thread -1297941584 (LWP 16400)]
 Adapting to Quadro hardware...
sh: line 1: egrep: command not found

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread -1220909360 (LWP 16367)]
0xb7d70708 in mallopt () from /lib/libc.so.6
(gdb) bt
#0 0xb7d70708 in mallopt () from /lib/libc.so.6
#1 0xb7d6f549 in free () from /lib/libc.so.6
#2 0xb7f1a10a in glXChannelRectSyncSGIX () from
/usr/lib/opengl/nvidia/lib/libGL.so.1
#3 0xb21b75a8 in ?? ()
#4 0xb7abbe85 in _nv000845gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#5 0xb21b75a8 in ?? ()
#6 0xb3bf2040 in ?? ()
#7 0x00000000 in ?? ()
#8 0x00009cef in ?? ()
#9 0x08549590 in ?? ()
#10 0x00000020 in ?? ()
#11 0xb3bf2040 in ?? ()
#12 0xb21b5550 in ?? ()
#13 0x00009cef in ?? ()
#14 0x08549590 in ?? ()
#15 0x00000000 in ?? ()
#16 0x00000000 in ?? ()
#17 0x00000000 in ?? ()
#18 0x00001ea8 in ?? ()
#19 0xb3c4560c in ?? ()
#20 0xb3c45654 in ?? ()
#21 0x08667278 in ?? ()
#22 0x00000000 in ?? ()
#23 0x00000000 in ?? ()
#24 0x00000000 in ?? ()
#25 0x00000000 in ?? ()
#26 0x00000003 in ?? ()
#27 0xb3c43570 in ?? ()
#28 0xb3c43570 in ?? ()
#29 0xb7abcb0b in _nv000845gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#30 0xb3bf2040 in ?? ()
#31 0xb3bf2040 in ?? ()
#32 0xb7ab24ca in _nv000845gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#33 0xb3bf2040 in ?? ()
#34 0xb3bf2040 in ?? ()
#35 0xb21b746c in ?? ()
#36 0xb21b746c in ?? ()
#37 0x00000000 in ?? ()
#38 0xb21b53d8 in ?? ()
#39 0xb3bf2040 in ?? ()
#40 0xb19eee68 in ?? ()
#41 0x00000000 in ?? ()
#42 0x00009cef in ?? ()
#43 0x08549590 in ?? ()
#44 0xb7f897db in ?? ()
#45 0x0818a92d in RepWireBondRender ()
#46 0xb19eee98 in ?? ()
#47 0xb19eee8c in ?? ()
#48 0xb2160a80 in ?? ()
#49 0x00000007 in ?? ()
#50 0x0888c748 in ?? ()
#51 0x00000000 in ?? ()
#52 0xb76e1307 in _nv000814gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#53 0xb3bf8f24 in ?? ()
#54 0xb3bf2040 in ?? ()
#55 0xb3bf8ed4 in ?? ()
#56 0xb3bf2040 in ?? ()
#57 0xb7964591 in _nv000851gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#58 0x080d528b in ObjectUseColor ()
#59 0xb2cf037f in ?? ()
#60 0x08112fab in CoordSetRender ()
#61 0xb2160a80 in ?? ()
#62 0x00000000 in ?? ()
#63 0x00000000 in ?? ()
#64 0x08549590 in ?? ()
#65 0x0886b930 in ?? ()
#66 0x00000000 in ?? ()
#67 0x00000000 in ?? ()
#68 0xbff9b468 in ?? ()
#69 0xbff9b4c4 in ?? ()
#70 0x00000007 in ?? ()
#71 0x0814725c in ObjectMoleculeRender ()
#72 0x0888c748 in ?? ()
#73 0x00000000 in ?? ()
#74 0x00000000 in ?? ()
#75 0x00000000 in ?? ()
#76 0x0886b930 in ?? ()
#77 0x08893df0 in ?? ()
#78 0xbff9b1ec in ?? ()
#79 0xbff9b49c in ?? ()
#80 0x08893df0 in ?? ()
#81 0x0867bf60 in ?? ()
#82 0x080fd178 in SceneRenderAll ()
#83 0x0886b930 in ?? ()
#84 0x00000000 in ?? ()
#85 0x00000000 in ?? ()
#86 0x00000000 in ?? ()
---Type <return> to continue, or q <return> to quit---
#87 0x00000000 in ?? ()
#88 0xbff9b49c in ?? ()
#89 0xbff9b4c4 in ?? ()
#90 0xbff9b48c in ?? ()
#91 0x00000000 in ?? ()
#92 0x086da0c8 in ?? ()
#93 0xb773e8c2 in _nv000812gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#94 0x08549590 in ?? ()
#95 0xbff9b49c in ?? ()
#96 0xbff9b4c4 in ?? ()
#97 0x00000000 in ?? ()
#98 0x00000000 in ?? ()
#99 0x00000000 in ?? ()
#100 0x00000000 in ?? ()
#101 0x086a6fec in ?? ()
#102 0xb2c7b008 in ?? ()
#103 0x00000000 in ?? ()
#104 0x000001f0 in ?? ()
#105 0x0000035c in ?? ()
#106 0x00000000 in ?? ()
#107 0x00000000 in ?? ()
#108 0xb7a7b9f5 in _nv000845gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#109 0x08667278 in ?? ()
#110 0x00000000 in ?? ()
#111 0x00000000 in ?? ()
#112 0x0000035c in ?? ()
#113 0x00000195 in ?? ()
#114 0x00000000 in ?? ()
#115 0x08667278 in ?? ()
#116 0x08675d00 in ?? ()
#117 0x00000000 in ?? ()
#118 0x00000003 in ?? ()
#119 0x0869b690 in ?? ()
#120 0x08668ad0 in ?? ()
#121 0x000001f0 in ?? ()
#122 0x0000035c in ?? ()
#123 0x08667278 in ?? ()
#124 0xb3b55c84 in ?? ()
#125 0x08668acc in ?? ()
#126 0x00000002 in ?? ()
#127 0x0869d408 in ?? ()
#128 0x08668b4c in ?? ()
#129 0x00000000 in ?? ()
#130 0xb78962b8 in _nv000840gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#131 0x003f5c84 in ?? ()
#132 0x08634f38 in ?? ()
#133 0x0866bb00 in ?? ()
#134 0x08667278 in ?? ()
#135 0x08675d00 in ?? ()
#136 0xb78968d4 in _nv000840gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#137 0xb7a61519 in _nv000851gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#138 0x00000000 in ?? ()
#139 0x08667278 in ?? ()
#140 0xb7a626f6 in _nv000851gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#141 0x08667278 in ?? ()
#142 0x0866bb00 in ?? ()
#143 0x085e66c8 in ?? ()
#144 0x00000000 in ?? ()
#145 0x086a8bf8 in ?? ()
#146 0x086a8bf8 in ?? ()
#147 0x00000280 in ?? ()
#148 0x000001e0 in ?? ()
#149 0x08660c7f in ?? ()
#150 0xb789691d in _nv000840gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#151 0x00000000 in ?? ()
#152 0xbff9b3ec in ?? ()
#153 0xbff9b4c4 in ?? ()
#154 0x3f2ccccc in ?? ()
#155 0x3e800000 in ?? ()
#156 0xbff9b48c in ?? ()
#157 0x00000402 in ?? ()
#158 0x00000001 in ?? ()
#159 0x00000001 in ?? ()
#160 0x43d59aca in ?? ()
#161 0x41a00000 in ?? ()
#162 0x08675d00 in ?? ()
#163 0xbff9b3ec in ?? ()
#164 0x08675cd0 in ?? ()
#165 0x00000000 in ?? ()
#166 0x00000000 in ?? ()
#167 0x00000000 in ?? ()
#168 0xf21a0000 in ?? ()
#169 0x402145a4 in ?? ()
#170 0x3faaaaab in ?? ()
#171 0x08667278 in ?? ()
#172 0xb7f1a33f in glXChannelRectSyncSGIX () from
/usr/lib/opengl/nvidia/lib/libGL.so.1
#173 0x086da0c8 in ?? ()
---Type <return> to continue, or q <return> to quit---
#174 0x08675d00 in ?? ()
#175 0xbff9b3ec in ?? ()
#176 0x08675cd0 in ?? ()
#177 0x08667278 in ?? ()
#178 0xb7f0bf6b in ?? () from /usr/lib/opengl/nvidia/lib/libGL.so.1
#179 0x08634f38 in ?? ()
#180 0x08675d00 in ?? ()
#181 0x00000001 in ?? ()
#182 0xb7f334e4 in _nv000658gl () from /usr/lib/opengl/nvidia/lib/libGL.so.1
#183 0x08675d00 in ?? ()
#184 0xbff9b3ec in ?? ()
#185 0x08675d00 in ?? ()
#186 0xbff9b3ec in ?? ()
#187 0xbff9b3ec in ?? ()
#188 0x08675d00 in ?? ()
#189 0xb78a6c21 in _nv000844gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#190 0xb78a6c86 in _nv000844gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#191 0x08667278 in ?? ()
#192 0xbff9b3ec in ?? ()
#193 0x08675d00 in ?? ()
#194 0x08667278 in ?? ()
#195 0x00004100 in ?? ()
#196 0x01f9b4a4 in ?? ()
#197 0x00000000 in ?? ()
#198 0x00000c00 in ?? ()
#199 0x00000000 in ?? ()
#200 0xb786dcf7 in _nv001092gl () from
/usr/lib/opengl/nvidia/lib/libGLcore.so.1
#201 0x08667278 in ?? ()
#202 0xbff9b3ec in ?? ()
#203 0x08675d00 in ?? ()
#204 0xb3bf2040 in ?? ()
#205 0x00000100 in ?? ()
#206 0x00004100 in ?? ()
#207 0x3f800000 in ?? ()
#208 0x0866bb00 in ?? ()
#209 0x08675d00 in ?? ()
#210 0x00000000 in ?? ()
#211 0xb3bf2040 in ?? ()
#212 0xb6e59a48 in ?? ()
#213 0x4b7fffff in ?? ()
#214 0x00000002 in ?? ()
#215 0x0000001f in ?? ()
#216 0x00000001 in ?? ()
#217 0x00000000 in ?? ()
#218 0x00000002 in ?? ()
#219 0xb6e59a58 in ?? ()
#220 0x00000000 in ?? ()
#221 0x00000000 in ?? ()
#222 0x01f0035c in ?? ()
#223 0xf1f00000 in ?? ()
#224 0x01f01000 in ?? ()
#225 0x00000058 in ?? ()
#226 0x00000000 in ?? ()
#227 0x00000000 in ?? ()
#228 0x00000000 in ?? ()
#229 0x3f800000 in ?? ()
#230 0x01010101 in ?? ()
#231 0x3f800000 in ?? ()
#232 0x00000000 in ?? ()
#233 0x000000ff in ?? ()
#234 0x00000000 in ?? ()
#235 0x08675d00 in ?? ()
#236 0x00000000 in ?? ()
#237 0x08675d00 in ?? ()
#238 0x00004100 in ?? ()
#239 0x00000000 in ?? ()
#240 0x00000000 in ?? ()
#241 0x00000000 in ?? ()
#242 0x3f800000 in ?? ()
#243 0xb3bf2040 in ?? ()
#244 0x3f5ed1c4 in ?? ()
#245 0x00000000 in ?? ()
#246 0x00000000 in ?? ()
#247 0xb3bf037f in ?? ()
#248 0x3f4ccccd in ?? ()
#249 0x3f4ccccd in ?? ()
#250 0x3f4ccccd in ?? ()
#251 0x3f800000 in ?? ()
#252 0xbe2aaaab in ?? ()
#253 0x3f955555 in ?? ()
#254 0x00000000 in ?? ()
#255 0x3f800000 in ?? ()
#256 0xbf000000 in ?? ()
#257 0x3f000000 in ?? ()
#258 0x00000000 in ?? ()
#259 0x00000000 in ?? ()
#260 0x0000035c in ?? ()
---Type <return> to continue, or q <return> to quit---
#261 0x000001f0 in ?? ()
#262 0x00000000 in ?? ()
#263 0x00000000 in ?? ()
#264 0x3f800000 in ?? ()
#265 0x00000000 in ?? ()
#266 0x00000000 in ?? ()
#267 0x00000000 in ?? ()
#268 0x3f800000 in ?? ()
#269 0x00000000 in ?? ()
#270 0x00000000 in ?? ()
#271 0x00000000 in ?? ()
#272 0x00000000 in ?? ()
#273 0x3f800000 in ?? ()
#274 0x080cc5dc in OrthoDoDraw ()
#275 0x08549590 in ?? ()
#276 0x00000000 in ?? ()
#277 0x00000000 in ?? ()
#278 0x00000000 in ?? ()
#279 0x00000000 in ?? ()
#280 0x08549590 in ?? ()
#281 0x085ce870 in ?? ()
#282 0x0000035c in ?? ()
#283 0xbff9b5b0 in ?? ()
#284 0x00000000 in ?? ()
#285 0x00000000 in ?? ()
#286 0x00000000 in ?? ()
#287 0xb7f6aed4 in pthread_mutex_lock () from /lib/libpthread.so.0
Previous frame inner to this frame (corrupt stack?)

Maybe that helps in tracking it down,
Sabuj Pattanayek

John Stone wrote:
> Sabuj,
> Did you try running VMD using the VMDSIMPLEGRAPHICS environment variable?
> Can you try that and tell me if that affects how it interacts
> with the nVidia drivers you've experienced problems with thus far?
> I'd like to know if it's related to the use of various OpenGL extensions
> or if the new nVidia drivers also fail on plain OpenGL 1.1 calls.
> Did you ever get a chance to email the bug to linux-bugs_at_nvidia.com?
> They provide a bug reporter script that they include with their drivers
> that provides the information they need about your Linux installation
> to help them fix the problem. Their bug reporting script is normally
> installed in:
> /usr/bin/nvidia-bug-report.sh
>
> It creates a nvidia-bug-report.log file they want you to mail to them.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, May 12, 2005 at 01:21:48PM -0500, Sabuj Pattanayek wrote:
>
>>Hi,
>>
>>Yes, I have found that 1.0.6629 for Quadros is the only version which
>>doesn't crash vmd and pymol on x86 (32bit) systems.
>>
>>ftp://download.nvidia.com/XFree86/Linux-x86/1.0-6629/NVIDIA-Linux-x86-1.0-6629-pkg1.run
>>
>>Hope that helps,
>>Sabuj Pattanayek
>>
>>Karsten Suhre wrote:
>>
>>>Hi,
>>>
>>>Is the problem you report with the NVIDIA driver only limitted to x86_64
>>>systems?
>>>
>>>My AMD Athlon 2400 bi-proc (32 bit SuSE 9.2 Nvidia Quadro vers. 1.0-7174) also
>>>crashes whenever I switch from Line mode to anything rendered. Does this mean
>>>that downgrading of the driver is the only solution?
>>>
>>>Thank you very much for your help,
>>>
>>>Kind regards,
>>>
>>>Karsten.
>>>
>>>
>>>On Thursday 12 May 2005 01:18, Sabuj Pattanayek wrote:
>>>
>>>
>>>>Hi,
>>>>
>>>>The latest x86_64 driver for linux used in a native 64bit environment
>>>>(kernel & system & vmd64):
>>>>
>>>>NVRM version: NVIDIA Linux x86_64 NVIDIA Kernel Module 1.0-7174
>>>>
>>>>..seems to work fine and doesn't have the problems that the 7xxx 32 bit
>>>>drivers have with 32 bit systems and vmd-32bit. In other words I can
>>>>recreate that problem if I use vmd32 in the 64bit environment.
>>>>Surprisingly the same is true for pymol64 and pymol32.
>>>>
>>>>You said you were running XP Pro on the athlon64 machine correct? You
>>>>may qualify for upgrading to winxp64
>>>>(http://www.microsoft.com/windowsxp/64bit/upgrade/default.mspx). Then
>>>>maybe you can try the 64bit nvidia driver? Or switching to linux64 may
>>>>be an option.
>>>>
>>>>..Sabuj Pattanayek
>>>>
>>>>Carlos Simmerling wrote:
>>>>
>>>>
>>>>>Hi John,
>>>>>I just got this sort of figured out but didn't know how to mail a
>>>>>reply to my own post. You're right, it's the nvidia drivers,
>>>>>not the athlon64. I had been using 71.84.
>>>>>
>>>>>I read another post about issues with the linux driver and quadros
>>>>>so I tried both a new leaked driver (76.50) and an old one (67.22).
>>>>>76.50 did not work but 67.22 does, so I think it might be the same
>>>>>quad strips problem you mentioned.
>>>>>thanks a lot for the quick reply!
>>>>>Carlos
>>>>>
>>>>>===================================================================
>>>>>Carlos L. Simmerling, Ph.D.
>>>>>Associate Professor Phone: (631) 632-1336
>>>>>Center for Structural Biology Fax: (631) 632-1555
>>>>>Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
>>>>>Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
>>>>>===================================================================
>>>>>
>>>>>John Stone wrote:
>>>>>
>>>>>
>>>>>>Hi Carlos,
>>>>>>What version of the nVidia drivers are you running on that
>>>>>>machine? Do you experience a crash with any other representation?
>>>>>>I've been hearing of some problems with nVidia drivers recently
>>>>>
>>>>>>from around the molecular graphics community (not just VMD), it's
>>>>>
>>>>>>possible that you're a victim of this recent phenomina.
>>>>>>What does VMD print in the text console when it first
>>>>>>starts up? If you can send me the startup messages, that would
>>>>>>be very helpful.
>>>>>>
>>>>>>Thanks,
>>>>>>John Stone
>>>>>>vmd_at_ks.uiuc.edu
>>>>>>
>>>>>>On Wed, May 11, 2005 at 09:13:25AM -0400, Carlos Simmerling wrote:
>>>>>>
>>>>>>
>>>>>>>Hi all,
>>>>>>>VMD is working fine on my pentium 4 PC under XP.
>>>>>>>I just got an Athlon64 PC (with XP) and a quadro FX1100.
>>>>>>>VMD works ok, but when I add a licorice representation it
>>>>>>>always crashed. The same thing works fine on my
>>>>>>>other (Intel) PCs under windows.
>>>>>>>
>>>>>>>Has anyone else seen this? I couldn't find anything
>>>>>>>in the archives, and the amd64 binaries seem to be for
>>>>>>>unixes only.
>>>>>>>
>>>>>>>Any ideas? I can send more info if it would help.
>>>>>>>Carlos
>>>>>>>
>>>>>>>--
>>>>>>>===================================================================
>>>>>>>Carlos L. Simmerling, Ph.D.
>>>>>>>Associate Professor Phone: (631) 632-1336
>>>>>>>Center for Structural Biology Fax: (631) 632-1555
>>>>>>>Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
>>>>>>>Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
>>>>>>>===================================================================
>
>